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Capturing the "Whole Tale" of Computational Research: Reproducibility in Computing Environments [article]

Bertram Ludaescher, Kyle Chard, Niall Gaffney, Matthew B. Jones, Jaroslaw Nabrzyski, Victoria Stodden, Matthew Turk
2016 arXiv   pre-print
We present an overview of the recently funded "Merging Science and Cyberinfrastructure Pathways: The Whole Tale" project (NSF award #1541450).  ...  Our approach has two nested goals: 1) deliver an environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and  ...  Acknowledgments Whole Tale is supported by NSF Award #1541450.  ... 
arXiv:1610.09958v1 fatcat:aivrazwadrhp7jy7dlc7n5zjby

Computing Environments for Reproducibility: Capturing the "Whole Tale" [article]

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+1 others)
2018 arXiv   pre-print
We report here on the design, architecture, and implementation of the Whole Tale environment.  ...  The Whole Tale focuses on the full spectrum of science, empowering users in the long tail of science, and power users with demands for access to big data and compute resources.  ...  Acknowledgments This research was supported by NSF grant 1541450: CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale.  ... 
arXiv:1805.00400v1 fatcat:xluy3bo3xzav3eoyetu34a2egy

Computing environments for reproducibility: Capturing the "Whole Tale"

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+2 others)
2018 Future generations computer systems  
Acknowledgments This research was supported by NSF, United States grant 1541450 (CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale).  ...  ., Computing environments for reproducibility: Capturing the ''Whole Tale'', Future Generation Computer Systems (2018), https://doi.org/10.1016/j.future.2017.12.029.  ...  ., Computing environments for reproducibility: Capturing the ''Whole Tale'', Future Generation Computer Systems (2018), https://doi.org/10.1016/j.future.2017.12.029. A.  ... 
doi:10.1016/j.future.2017.12.029 fatcat:quttkpfzkfamrlapqj4c7ykk64

Publishing Transparent & Reproducible Computational Research with Whole Tale

Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew Jones, Kacper Kowalik, Sara Lambert, Bertram Ludäscher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen (+2 others)
2022 Zenodo  
Tale Whole Tale (WT) from the user's perspective WT roles in the science community Elements of a Tale Publishing a Tale to DataONE, Globus, Zenodo, … o Tale = executable research object that captures  ...  , publishing & verifying computational research artifacts (which we call tales) o Whole Tale = Infrastructure + Education + Outreach * #1541450: Merging Science & Cyberinfrastructure Pathways: The Whole  ...  Re-execute in Whole Tale • Web-based platform for interactive and exploratory data-driven and computational-analysis using popular environments (JupyterLab, RStudio, MATLAB, Stata) • Versioning, sharing  ... 
doi:10.5281/zenodo.6859457 fatcat:zvgequh4dbfs7mpfnlf2ki5ejm

Telling the Whole Tale via Reproducible Data Reuse

Matthew B. Jones
2019 Zenodo  
Whole Tale provides a mature platform for reproducible research that preserves code, data, and compute environments in a manner that allows other researchers to interpret and re-use all products of research  ...  These archived 'tales' can be run on the Whole Tale platform by other researchers, or can be downloaded and run locally through Docker-based execution environments saved in the tale.  ...  IMS Bulletin Simplifying Computational Reproducibility in Whole TaleResearchers can easily package and share tales: ○ Data, Code, and Compute Environment ○ to re-create the computational results from  ... 
doi:10.5281/zenodo.3471934 fatcat:xmziuhnvwbewlbeu4iyltwmtja

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3381754 fatcat:fbhbghrruvhxlipbiwz5oqtete

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3271763 fatcat:fy7s42fembgg5dafpvfyrw3qpe

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3268966 fatcat:hzc2qosshjcydb7z4fhigvuzke

Publishing computational research – A review of infrastructures for reproducible and transparent scholarly communication [article]

Markus Konkol, Daniel Nüst, Laura Goulier
2020 arXiv   pre-print
The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results.  ...  This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.  ...  The authors of this paper are members of the o2r project that was also discussed in this paper (http://o2r. info/).  ... 
arXiv:2001.00484v1 fatcat:4nm6pmwzhvgptmcfhbkp7efvky

Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

Markus Konkol, Daniel Nüst, Laura Goulier
2020 Research Integrity and Peer Review  
We reviewed 11 applications that can assist researchers in adhering to reproducibility principles.  ...  The applications were found through a literature search and interactions with the reproducible research community.  ...  Acknowledgements We thank Timothy Errington and Mario Malicki for their reviews, Vicky Steeves for a helpful discussion on the article preprint [39] , and Celeste Brennecka for proofreading.  ... 
doi:10.1186/s41073-020-00095-y pmid:32685199 pmcid:PMC7359270 fatcat:clovjhifpnc2lpol7yr2mv4v5e

Advancing computational reproducibility in the Dataverse data repository platform [article]

Ana Trisovic, Philip Durbin, Tania Schlatter, Gustavo Durand, Sonia Barbosa, Danny Brooke, Mercè Crosas
2020 arXiv   pre-print
This paper addresses the shortcomings of data repositories and reproducibility tools and how they could be overcome to improve the current lack of computational reproducibility in published and archived  ...  One of their conclusions was that the way data repositories store research data and code cannot fully facilitate reproducibility due to the absence of a runtime environment needed for the code execution  ...  ACKNOWLEDGMENTS Thank you to the Dataverse team for their help and support. This work is partially funded by the Sloan Foundation. Ana Trisovic is funded by the Sloan Foundation.  ... 
arXiv:2005.02985v2 fatcat:rfegdysbufc2jeb324slnmeqay

CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

Daniel Nüst, Stephen J. Eglen
2021 F1000Research  
The traditional scientific paper falls short of effectively communicating computational research.  ...  While CODECHECK has clear limitations, it may represent a building block in Open Science and publishing ecosystems for improving the reproducibility, appreciation, and, potentially, the quality of non-textual  ...  We thank Antonio Páez (Journal of Geographical Systems) for enabling CODECHECKs, Carlos Granell and Frank Ostermann for contributing certificates as reproducibility reviewers at the AGILE conference, and  ... 
doi:10.12688/f1000research.51738.1 pmid:34367614 pmcid:PMC8311796 fatcat:rxh2hekl3ffk3owa75fose4th4

Building a Vision for Reproducibility in the Cyberinfrastructure Ecosystem: Leveraging Community Efforts

2020 Supercomputing Frontiers and Innovations  
The work also articulates avenues for future research at the intersection of transparency, reproducibility, and computational infrastructure that supports scientific discovery.  ...  The scientific computing community has long taken a leadership role in understanding and assessing the relationship of reproducibility to cyberinfrastructure, ensuring that computational results -such  ...  This paper is distributed under the terms of the Creative Commons Attribution-Non Commercial 3.0 License which permits non-commercial use, reproduction and distribution of the work without further permission  ... 
doi:10.14529/jsfi200106 fatcat:65ngkgmfqjacbb2llj3exmpkei

CODECHECK: An Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

Daniel Nüst, Stephen J Eglen
2021 Zenodo  
Preprint of CODECHECK paper.  ...  We thank Antonio Páez (Journal of Geographical Systems) for enabling CODECHECKs, Carlos Granell and Frank Ostermann for contributing certificates as reproducibility reviewers at the AGILE conference, and  ...  Brennecka from the Scientific Editing Service, University of Münster, for her editorial review. Author contributions DN and SJE contributed equally to all aspects of this project.  ... 
doi:10.5281/zenodo.4593367 fatcat:escmjonjjfft7jnr2waivj422u

Toward Enabling Reproducibility for Data-Intensive Research using the Whole Tale Platform [article]

Kyle Chard, Niall Gaffney, Mihael Hategan, Kacper Kowalik, Bertram Ludaescher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2020 pre-print
Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community  ...  We describe opportunities, challenges, and solutions to facilitating reproducibility for data- and compute-intensive research, that we call "Tales at Scale," using the Whole Tale computing platform.  ...  The goal of the Whole Tale project is to enable reproducibility for computation-and data-enabled research.  ... 
doi:10.3233/apc200107 arXiv:2005.06087v1 fatcat:2pjndo4y4bcxjnvx3onfqlozlq
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